The taxonomic status of the Chilean blue mussel Mytilus chilensis has been controversial for decades because of its phenotypic and genetic proximity to other species of the genus Mytilus from both hemispheres. This study reports the development of nine polymorphic microsatellite markers from the M. chilensis genome. The number of alleles per locus ranged between four and nine, and the observed heterozygosity ranged from 0.182–0.750 in a wild sample of 24 individuals from Caicaén (Chiloé Region, Chile). Lack of efficient amplification of many of these microsatellite loci in other Mytilus species suggests that M. chilensis is a valid, distinct species within the genus. These new markers would be useful in fine-scale population analyses of M. chilensis as well in the aquaculture management of this marine resource.